Long Noncoding RNAs AC009014.3 and Newly Discovered XPLAID Differentiate Aggressive and Indolent Prostate Cancers

Anthony J Cesnik,Bing Yang,Andrew Truong,Tyler Etheridge,Michele Spiniello,Maisie I Steinbrink,Michael R Shortreed,Brian L Frey,David F Jarrard,Lloyd M Smith

doi:10.1016/j.tranon.2018.04.002

Anthony J Cesnik, Bing Yang + Show 8 more

Open Access

https://doi.org/10.1016/j.tranon.2018.04.002

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Journal: Translational oncology	Publication Date: May 1, 2018
Citations: 7	License type: cc-by

Affiliation: University of Wisconsin–Madison

Abstract

INTRODUCTION: The molecular mechanisms underlying aggressive versus indolent disease are not fully understood. Recent research has implicated a class of molecules known as long noncoding RNAs (lncRNAs) in tumorigenesis and progression of cancer. Our objective was to discover lncRNAs that differentiate aggressive and indolent prostate cancers. METHODS: We analyzed paired tumor and normal tissues from six aggressive Gleason score (GS) 8-10 and six indolent GS 6 prostate cancers. Extracted RNA was split for poly(A)+ and ribosomal RNA depletion library preparations, followed byRNA sequencing (RNA-Seq) using an Illumina HiSeq 2000. We developed an RNA-Seq data analysis pipeline to discover and quantify these molecules. Candidate lncRNAs were validated using RT-qPCR on 87 tumor tissue samples: 28 (GS 6), 28 (GS 3+4), 6 (GS 4+3), and 25 (GS 8-10). Statistical correlations between lncRNAs and clinicopathologic variables were tested using ANOVA. RESULTS: The 43 differentially expressed (DE) lncRNAs between aggressive and indolent prostate cancers included 12 annotated and 31 novel lncRNAs. The top six DE lncRNAs were selected based on large, consistent fold-changes in the RNA-Seq results. Three of these candidates passed RT-qPCR validation, including AC009014.3 (P < .001 in tumor tissue) and a newly discovered X-linked lncRNA named XPLAID (P = .049 in tumor tissue and P = .048 in normal tissue). XPLAID and AC009014.3 show promise as prognostic biomarkers. CONCLUSIONS: We discovered several dozen lncRNAs that distinguish aggressive and indolent prostate cancers, of which four were validated using RT-qPCR. The investigation into their biology is ongoing.

Highlights

The molecular mechanisms underlying aggressive versus indolent disease are not fully understood
We developed a workflow for global analysis of long noncoding RNAs (lncRNAs) using deep RNA sequencing (RNA-Seq) data
Materials and Methods This study focuses on identifying novel lncRNAs that differentiate aggressive and indolent prostate cancers using RNA sequencing data collected from primary tissue samples

Summary

Introduction

The molecular mechanisms underlying aggressive versus indolent disease are not fully understood. Several studies have examined prostate cancer cell lines or cohorts of tumor specimens to find genomic variants [4], DNA methylation patterns [5], RNA-binding proteins [6], gene expression [7], or protein expression patterns [8,9] that are characteristic of aggressive or indolent cancers. Another promising avenue towards an understanding of the differences between these cancers is identifying and characterizing long noncoding RNAs (lncRNAs).

Objectives

Methods

Results